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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaaacttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG

Basic information

species Vitis vinifera
transcript Vv05s0020g00880.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaa-acttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG
                      |       || |  || || ||  || | ||  | || || | |  |   || || || | ||  || |    | | | | |    ||||| ||||||||||| ||||| || ||||| |||||||| ||||||||||| || || |||||||| || ||||| ||||||
----------------------gtgagtggttatggttttgcagtggtgaatattattttatgagcccaaa-ttttatctgtgta-aatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 16
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaa-acttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG---------------------
                      |       || |  || || ||  || | ||  | || || | |  |   || || || | ||  || |    | | | | |    ||||| ||||||||||| ||||| || ||||| |||||||| ||||||||||| || || |||||||| || ||||| ||||||                     
----------------------gtgagtggttatggttttgcagtggtgaatattattttatgagcccaaa-ttttatctgtgta-aatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAGGTAATTGCAAAACTCTAGATG

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 15
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaaacttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG
                     |   | |||  ||| |||||         || | ||  ||    | |   | ||   || ||||    ||    | || ||   ||||||| |||||||||||||| || |||||||| ||||||||  |  ||||||||||||| |||||||| | ||| |||||||||
--------------------gtatgtgcttacttttttatgacc------ctgatctctattttatcacattactcttttgatattgaactgtttaaattttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaaacttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG
                   | ||  ||  |  || |||||  | ||    || | ||  ||    | |   | ||   || |||     ||    | || |   | |||||| |||||||||||||| || |||||||| ||||||||  |  ||||||||||||| |||||||| | ||| |||||||||
----------------gtatgtggtttagtggttacttattgatgacc--ctgatctctattttatcacattactcttttgatactgaactgtttaaatttatta-ttgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 14
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaaacttcataaactaagggttctacctttatatgatcc-ttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG
   | || | || ||||   |  ||     | | | ||||         || | ||||   |            | | |  | |||| |  ||  ||| | || |||||| |||||||| ||||| || |||||||| || ||||||||  || |||| ||||| ||||||||||||  ||| |||||||||
--gtatgttatttcttctagacacccctgatctctattat---------accagactttgca----------ctttcttgaaaatgaactgtttaaatttatttcaattgtagGTATGCAGATATATATACCTCTAGAGTGTCAAATTTTTTATATTACACACCGTTTATGTATTTTGGCTCTCAGGAACAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|352773983|gb|FQ473115.1|FQ473115
EST:     TCACGTGCGGGTCTTTGGGATAAAAGTCACTTGATGAGACAAATTGAAAA                         GTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACC
genomic: TCACGTGCGGGTCTTTGGGATAAAAGTCACTTGATGAGACAAATTGAAAAgtatgtgctt ... ccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACC
EST: gi|352772409|gb|FQ469934.1|FQ469934
EST:     TCACGTGCGGGTCTTTGGGATAAAAGTCACTTGATGAGACAAATTGAAAA                         GTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACC
genomic: TCACGTGCGGGTCTTTGGGATAAAAGTCACTTGATGAGACAAATTGAAAAgtatgtgctt ... ccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG
                              tccttac  putative branch site (score: 2)
                                       tatcttcc  putative PPT
                     tttatatgat  TA-rich tract